A pupil at Porthcawl Primary School is being treated for a suspected case of meningococcal meningitis at the University of Wales Hospital in Cardiff.
In a separate incident, a teenaged boy from Glanafan Comprehensive School in Port Talbot is at another hospital, believed to be suffering from the same disease.
Meanwhile in Swansea, an eight-year-old pupil at Brynmill Primary School is in hospital with viral meningitis, a less serious form of the
disease.
Iechyd Morgannwg Health Authority reassured parents of pupils at the three schools that all appropriate action was being taken.
It also warned anyone who suspected their child might be showing symptoms of the disease to seek immediate medical help.
Close observation
Dr Ronan Lyons, a consultant in public health medicine with the authority, confirmed that the Glanafan pupil was "a probable case of meningococcal disease", and was responding well to treatment.
He added that the second youngster from Porthcawl was being treated for "probable meningococcal meningitis" and was also under close observation.
In a separate statement, the health authority said the condition of the Swansea youngster with viral meningitis was being monitored closely and was improving all the time.
"We know that this particular child is improving in hospital," a spokesman said.
Antibiotics used
"He has a form of meningitis, but it is not meningococcal, and is less serious."
All three children had been treated with antibiotics to remove the organism from the nose and throat and prevent the spread of further infection.
Parents are being urged to watch for the tell-tale signs of meningitis.
They include headache, fever, vomiting, neck stiffness, dislike of light, and drowsiness.
The most distinctive sign is a rash which does not disappear when pressed with a glass tumbler.